1. Experiment Health for: DIA-NN Sheep Plasma

The experiment contains 60 samples; the condition of interest has 2 categories: vehicle, vitaminC.

A.Dimensionality reduction

The data have been log2 transformed and imputed using the MNAR imputation method before PCA.

PCA

MDS

B. Quantitative values CV distributions

2. Intensity distribution across runs

Imputed data

Initial data

3. Feature completedness

By sample

By protein

4. Imputed versus non imputed log2 Intensity values

5. Model QC

Volcano plots

MA plot

Histogram of pvalues

## $breaks
##  [1] 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
## 
## $counts
##  [1] 192  55  35  30  37  19  23  23  16  29
## 
## $density
##  [1] 4.1830065 1.1982571 0.7625272 0.6535948 0.8061002 0.4139434 0.5010893 0.5010893 0.3485839 0.6318083
## 
## $mids
##  [1] 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95
## 
## $xname
## [1] "stats[, pval]"
## 
## $equidist
## [1] TRUE
## 
## attr(,"class")
## [1] "histogram"